No output produced from searching against known motif database in CentriMo
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5 months ago
greyman ▴ 160

I am using MEME suite to find some information about TF motif site from a list of TSS upstream sequence that I got. The DNA sequence is generated from a non-model organism, which is also a crustacean. As I dont have a control set, I simply input with the "primary sequence (fasta sequence)" and "output from MEME (motif that I am interested)" to do the local enrichment with option "anywhere". I got some output with most of it showed e-value as 1 and p-value as 9. This doesn't seemed good instead of using "MEME output", I swapped it with fly database, yet it produced nothing. I have also tried with eukaryote database, JASPAR2018_core_vertebrate and jaspar2018_core_insect, they all showed nothing in the output. Is there any advise on how to make this motif findings meaningful using CentriMo? I know that simply relying on the output of MEME is not enough because many false positives results is generated at the same time. Instead of MEME if I straight away proceed with TOMTOM, is this makes sense since I can argue that the sequence called by MEME showed high similarity to consensus sequence found by TOMTOM? Thank you in advance.

centrimo motif meme tomtom TFBS • 394 views
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What is the predicted motif length by MEME. To check the short motif enrichment you can use STREME (DREME is deprecated).

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Thanks for the reply. I have multiple files which contain different sequences which represents different gene sets. While each files has more than 100 sequences(each sequence 3k bases), STREME gives me a list of motif discovered for each file ( default setting 8-15 for length). Since they are already enriched, I guess the next step is to examine them with TOMTOM and skip CentriMo?

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TOMTOM and CentriMo, serve different purposes. TOMTOM is for aligning the predicted motifs with known motifs (you can relate it with a BLAST in sequence alignment) and find out the similarity whereas CentriMo predicts the density of the given motif in a specific region of the target sequence.

Let's say TOMTOM gives you an idea about the class/type of the motif whereas CentriMo gives you a gist of how that motif is distributed in your sequence.

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